Merge branch 'release/v2.2.0'

Author: CiaranOMara

.cirrus.yml

@@ -0,0 +1,26 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "2"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main(master_branch = "master")
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/CompatHelper.yml

@@ -0,0 +1,17 @@
+name: TagBot
+
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/TagBot.yml

@@ -0,0 +1,45 @@
+name: Unit Tests
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  test:
+    name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }} - ${{ matrix.julia-arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version:
+          - '1.0' # LTS
+          - '1'
+        julia-arch: [x64, x86]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+        exclude:
+          - os: macOS-latest
+            julia-arch: x86
+        experimental: [false]
+        include:
+          - julia-version: nightly
+            julia-arch: x64
+            os: ubuntu-latest
+            experimental: true
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Run Tests
+        uses: julia-actions/julia-runtest@v1
+      - name: Create CodeCov
+        uses: julia-actions/julia-processcoverage@v1
+      - name: Upload CodeCov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ${{ steps.coverage-processing.outputs.lcov-file }}
+          fail_ci_if_error: false

.github/workflows/UnitTests.yml

@@ -1,190 +1,24 @@
+# Files generated by invoking Julia with --code-coverage
 *.jl.cov
 *.jl.*.cov
-*.jl.mem
-### JetBrains template
-# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
-# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
-
-/.idea
-
-# User-specific stuff
-.idea/**/workspace.xml
-.idea/**/tasks.xml
-.idea/**/dictionaries
-.idea/**/shelf
-
-# Sensitive or high-churn files
-.idea/**/dataSources/
-.idea/**/dataSources.ids
-.idea/**/dataSources.local.xml
-.idea/**/sqlDataSources.xml
-.idea/**/dynamic.xml
-.idea/**/uiDesigner.xml
-
-# Gradle
-.idea/**/gradle.xml
-.idea/**/libraries
-
-# CMake
-cmake-build-debug/
-cmake-build-release/
-
-# Mongo Explorer plugin
-.idea/**/mongoSettings.xml
-
-# File-based project format
-*.iws
-
-# IntelliJ
-out/
-
-# mpeltonen/sbt-idea plugin
-.idea_modules/
-
-# JIRA plugin
-atlassian-ide-plugin.xml
-
-# Cursive Clojure plugin
-.idea/replstate.xml
-
-# Crashlytics plugin (for Android Studio and IntelliJ)
-com_crashlytics_export_strings.xml
-crashlytics.properties
-crashlytics-build.properties
-fabric.properties
-
-# Editor-based Rest Client
-.idea/httpRequests
-### Linux template
-*~
-
-# temporary files which can be created if a process still has a handle open of a deleted file
-.fuse_hidden*
-
-# KDE directory preferences
-.directory
-
-# Linux trash folder which might appear on any partition or disk
-.Trash-*
-
-# .nfs files are created when an open file is removed but is still being accessed
-.nfs*
-### Eclipse template
-
-.metadata
-bin/
-tmp/
-*.tmp
-*.bak
-*.swp
-*~.nib
-local.properties
-.settings/
-.loadpath
-.recommenders
-
-# External tool builders
-.externalToolBuilders/
-
-# Locally stored "Eclipse launch configurations"
-*.launch
 
-# PyDev specific (Python IDE for Eclipse)
-*.pydevproject
-
-# CDT-specific (C/C++ Development Tooling)
-.cproject
-
-# CDT- autotools
-.autotools
-
-# Java annotation processor (APT)
-.factorypath
-
-# PDT-specific (PHP Development Tools)
-.buildpath
-
-# sbteclipse plugin
-.target
-
-# Tern plugin
-.tern-project
-
-# TeXlipse plugin
-.texlipse
-
-# STS (Spring Tool Suite)
-.springBeans
-
-# Code Recommenders
-.recommenders/
-
-# Scala IDE specific (Scala & Java development for Eclipse)
-.cache-main
-.scala_dependencies
-.worksheet
-### Vim template
-# Swap
-[._]*.s[a-v][a-z]
-[._]*.sw[a-p]
-[._]s[a-v][a-z]
-[._]sw[a-p]
-
-# Session
-Session.vim
-
-# Temporary
-.netrwhist
-# Auto-generated tag files
-tags
-### macOS template
-# General
-.DS_Store
-.AppleDouble
-.LSOverride
-
-# Icon must end with two \r
-Icon
-
-# Thumbnails
-._*
-
-# Files that might appear in the root of a volume
-.DocumentRevisions-V100
-.fseventsd
-.Spotlight-V100
-.TemporaryItems
-.Trashes
-.VolumeIcon.icns
-.com.apple.timemachine.donotpresent
-
-# Directories potentially created on remote AFP share
-.AppleDB
-.AppleDesktop
-Network Trash Folder
-Temporary Items
-.apdisk
-### Windows template
-# Windows thumbnail cache files
-Thumbs.db
-ehthumbs.db
-ehthumbs_vista.db
-
-# Dump file
-*.stackdump
-
-# Folder config file
-[Dd]esktop.ini
-
-# Recycle Bin used on file shares
-$RECYCLE.BIN/
-
-# Windows Installer files
-*.cab
-*.msi
-*.msix
-*.msm
-*.msp
+# Files generated by invoking Julia with --track-allocation
+*.jl.mem
 
-# Windows shortcuts
-*.lnk
+# System-specific files and directories generated by the BinaryProvider and BinDeps packages
+# They contain absolute paths specific to the host computer, and so should not be committed
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# Build artifacts for creating documentation generated by the Documenter package
+docs/build/
+docs/site/
+
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml

.gitignore

@@ -1,7 +1,7 @@
 name = "Bedgraph"
 uuid = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd"
 authors = ["Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "2.1.0"
+version = "2.2.0"
 
 [compat]
 julia = "0.7, 1"